Two of the major pathways involved in induced defense of plants against pathogens include the salicylic acid (SA)- and jasmonic acid (JA)-mediated pathways that act mainly against biotrophs and necrotrophs, respectively. However, some necrotrophic pathogens, such as Botrytis cinerea, actively induce the SA pathway, resulting in cell death that allows the pathogen to proliferate in the plant. Starting from an isogenic canola (Brassica napus) line, epilines were selected with a reduced sensitivity to SA. The genes belonging to the SA pathway had an altered transcription profile in the SA-tolerant lines, when treated with SA. Besides the already known genes of the SA pathway, new SA target genes were identified, creating possibilities to better understand the plant defense mechanism against pathogens. The SA-tolerant line with the lowest SA-induced gene expression is tolerant to Botrytis cinerea. When treated with SA, this line has also a reduced histone modification (histone H3 lysine 4 trimethylation) at the genes at the start of the SA pathway.